I had to reboot to get rid of the emulated XBOX 360 controller from Touchmote to go away and now all of my controller work like they should. I could get it to work if I switch the controller from X to direct input, but then my XBOX One controller would still not work and I wanted to use both controllers. Well it didn’t, and the driver was still active causing Retroarch to choose that 360 driver Instead of my Logitech controller. Touchmote is supposed to dump any connections to any Wiimotes and shut down the emulated XBOX 360 controller driver when I tell it to. All of the sudden I found that my controller would not work in Retroarch after recently using Touchmote. Some programs like one of my favorites, Touchmote emulates an XBOX 360 controller.
The first thing I would do is check your devices. I’ve had problems like this before and it’s always because of Retroarch choosing what it thinks is a controller over the one you’re using.